Nowadays, there are many complete genomic sequences available for bacteria, allowing comparison between them and thus allowing the evolution of bacteria to be understood i.e/ the creation of taxonomic groups and a phylegeneic tree

However, as bacteria are continually exchanging genes, plasmids or entire chromosomes (by conjugation, transformation etc), is the correct phylogenic tree or taxonomy available through genomic analysis?

First however much complte genome sequences there are they are scarcely a drop of water in the ocean compared to the number of bacterial species, not even talking about diversity in one species (Compare K12 and O157:H7 genome, 2 E. coli, 20% more genome in o157:H7). So we are far from having enough data to build a significant tree.
But the point you raise about what is usually reffered to as horizontal transfer is not a recent one and that is why phylogeneies are more interested in the housekeeping genes than in the other genes, probably less stable.

And this just point out how difficult it is to define what is indeed a bacterial species. And so much for the "real tree of life".

In fact there is a lot more to say about horizontal transfer and phylogeny, but I think I do not feel like writing a complete review on the subject. I have a few references that I will try to dig oout from my stacks of papers but, please be patient

Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)